Besides that, I don't think knowing HTTP headers or understanding significance of trailing newlines is required to write CGI scripts. You only need to know that you need those three 'magic' lines in the front of your scripts. Similarly like you need to know that in php you need <?php ... ?> around your script.
PHP "is especially suited for Web development and can be embedded into HTML" [1]. Python "lets you work more quickly and integrate your systems more effectively" [2]. They can both do the task of the other, but the upstart time for a developer to handle the task of making a web app is smaller for PHP.
I've never taken the non-framework approach with python for anything significant, but how does it handle cookies, GET and POST fields, sessions, and file uploads? In PHP you'd have $_COOKIE, $_GET, $_POST, $_SESSION, and $_FILES as built-in global variables.
Are these differences still insignificant?
[1] http://php.net/ [2] http://python.org/
But, er. Does this really matter? Yes, you can get "hello world" in PHP with one line of not-PHP. You can also get "hello world" in Python + Flask with seven lines, and you'll get half a dozen extremely nice features for free that you can learn about as you go.
Arguing about what stack has the simplest way to build from total scratch is a sad race to the bottom. I'd rather be making the point that rich Web development can be easy, not that cobble-your-own-thing-together-with-duct-tape can be easy.
So yes, it really does matter in the context of this thread. On the whole I agree with your philosophy that frameworks are there for a reason: you get many features for almost nothing.
But sometimes you just don't need a framework, you need something quick-and-dirty that just works.
Don't get me wrong, I would never choose to write a web app in PHP over python. But it is brain dead simple to go from nothing to something in a few keystrokes. Which is precisely what people just learning to write web apps want (right or wrong).
[1] I can't remember how long it took me to figure out that I needed the second CRLF after the "Content-Type: text/html" when I was learning perl (or even the fact that I needed to specify the Content-Type in the first place).